Considering the VC is for all intents and purposes an emulator? I don't see why they wouldn't. Remember, GF/Nintendo essentially went: "For a Pokémon to be accepted through Pokémon Bank, it must fill these and these parameters; if not, it gets rejected" as the only safety measure against transferring over Glitch Mons (and even that was not perfect: if a glitched Mew was further glitched/'hacked' to also have the correct Event tags, it was accepted just fine.). I'm assuming that all they cared about was the thing not getting onto the main games and per extension Wonder Trade; whatever you did to your copy of the games was your problem.
Well I also wouldn't count mew as a "glitched mon". It's obtainable through a glitch, but you can use that same glitch to encounter any species of pokemon in the game's memory. And that's all that the Mew glitch is -- using a glitch to create an encounter with a species of pokemon that would've otherwise just been unused data. Nothing else about the game counts it as a glitch pokemon.
When I think about filters designed to keep glitch pokemon out, I'm assuming we're talking, like... Missingno. And 'M. And h poke. And LM4. And all the lovely little abominations with completely unpronounceable names.
Because, I mean, if you transfer a Mew into Bank, then, at worst, you're called a cheater. But if you were able to get a Missingno (much less any of the far more unstable glitches) into Bank, well... that has the potential to be literally game-breaking. As fascinating as it would be to see what Missingno can do to a Gen VI or VII game, I can understand why Gamefreak would want to block it.
Now I don't know exactly how that glitch will work, but there's a good chance that it will require some extra glitching and stuff for the system to count it as legit (assuming they haven't learned from their mistakes and are planning to outright block Celebi period, regardless of how legit it would look. But eh, we can all hope, right? ^_^
"Learning from their mistakes" implies that they were completely caught off-guard by people using the Mew glitch to get a valid Mew into Bank in the first place. And I find it very difficult to believe that no one saw that coming. It's not exactly an obscure glitch.
Anyway, apparently the Mew from the Mew glitch counts as legit because the glitch triggers a battle that counts as a "fateful encounter" (in other words, an event) as far as the game is concerned. ...Which is interesting. Meanwhile the Celebi glitch in G/S works by leaving a pokemon at the day care, and then, after doing some glitchy stuff, you go back to the day care, and suddenly your pokemon is a Celebi. So, yeah, it might be harder to make that count as legit.
I'm curious as to what would happen if I tried to transfer anything to Bank while I have that glitch egg in my game... for whatever reason, I was able to use that egg to bypass the filter used by G/S that's supposed to prevent glitch pokemon from being traded. And, like, I don't mean that I traded the egg. I mean that just having the egg in my party let me trade all sorts of glitches. ...So yeah, this has the potential to be... interesting...
Again, I see no reason why they shouldn't.
The thing about the coin case glitch (or at least, this version of it) is that, firstly, it doesn't work on a regular Gameboy. You have to be using Gameboy Color, or Advanced, or really any model that's equivalent to the Color or higher. The coin case glitch works by forcing the game to soft-reset, and then, for whatever reason, it bypasses whatever check the game does that tells it what model of Gameboy it's running on -- so then it loads as if it's running on a regular Gameboy, when it's actually running on a Color/Advanced/whatever. And this mix-up causes all the colors in the game to get all wonky. (It also, interestingly enough, reveals full-color versions of Ho-Oh and Lugia on the games' title screens, even though they're normally only silhouettes in regular gameplay.)
So, yeah, I guess it theoretically wouldn't work if the VC counts as a regular Gameboy as opposed to a higher model. o_o Or... maybe it would count as a different model of Gameboy entirely, thus keeping the glitch intact? Who knows.
That being said, the coin case glitch is extremely varied and has lots of different uses -- many of which don't cause any forced soft resets like this. (And even if a version of the coin case glitch
did force the game to soft reset, theoretically I suppose you would still get whatever your desired result was, just without the weird colors...)
And on a miscellaneous note about the LSD coin case glitch: attempting to do it on Crystal version gets you a surprisingly-detailed error screen that essentially says "this cartridge can only be played on a Gameboy Color", which is... true, since Crystal, unlike Gold and Silver, is actually a GBC game, and not a regular Gameboy game. But, the shape of GBC cartridges leaves them incapable of fitting inside a regular Gameboy, so... I find it interesting that such an interesting-looking error screen exists, despite the fact that it can literally only appear when you trick the cartridge into thinking that it's running on a regular Gameboy when it really isn't.
I also remember being very confused when I accidentally caused that to happen to my Crystal version as a kid. XD